"Rust is a shifty, changing, constantly evolving enemy. We can never lower our guard. We must fight rust by all means open to science."

—E. C. Stakman (1937)

The challenge     

Stem rust has been the cause of devastating epidemics throughout history, because under the right conditions for disease development it can cause 50-100% yield loss. Resistance to particular rust “races” can be provided by single resistance genes in the plant that recognize specific rust effectors, but the fungus quickly evolves to evade this recognition. In the 1950’s, new wheat strains resistant to stem rust were developed and distributed throughout the world as part of the Green Revolution. However, in 1999 a new strain of stem rust arose in Uganda (termed Ug99 for its country of origin) that overcame the resistance of existing wheat lines. Since then, Ug99 has been spreading through East Africa into the Middle East.

Two other important wheat rust pathogens, stripe (yellow) rust and leaf rust, also cause significant annual losses wherever wheat is grown.

Wheat stem rust in the field

Wheat Stem rust in the field. Photo courtesy of Dr. Evans Lagudah, CSIRO Agriculture

The strategy

While any one resistance gene can be easily overcome, a combination of multiple genes (a “stack) requires multiple changes in the pathogen to occur at once. A stack of 3-5 effective resistance genes has a very small chance of being overcome. Recently, several resistance genes against Ug99 have been cloned by our collaborators and others, and many more are in the process of being isolated. Our goal is to combine several isolated resistance genes and work with partners to introduce them together into preferred varieties of wheat.  A similar strategy would be effective against stripe and leaf rusts, and 2Blades is also working with collaborators to identify resistance genes effective against these diseases.

The science

Pathogen recognition by resistance genes

Pathogens including rusts introduce a variety of effectors into the host cell to alter the host metabolism to benefit the pathogen or to suppress host defense responses, and many plant resistance proteins recognize those effectors or their secondary effects. If an effector is recognized by a resistance protein in the plant, then the infection can be stopped or slowed, and the plant will be resistant to that pathogen. However, if an effector can be changed or lost without affecting the virulence of the pathogen, then new pathogen races lacking it can be selected. The majority of resistance genes against wheat rusts are race-specific, meaning that they recognize some races of the pathogen but not others, based on the effectors present in each race. Most race-specific resistance genes against rusts are of the NB-LRR type. 2Blades has pioneered a technique for rapidly isolating these NB-LRR resistance genes.

A second type of resistance gene found in wheat is known as an adult plant resistance (APR) gene. These genes are not specific to a given race of rust, and are often effective against multiple rust species.  While resistance mediated by APR genes is generally only partial, it can be significant. Stacking both race-specific and APR genes may provide even more durability.

Rust fungi

Maintaining resistance to rust fungi is challenging because of the nature of the pathogen. When growing on wheat, stem rust produces 100 billion spores per hectare, or around 19 kg/ha of spores! These spores can be spread by wind over long distances. The spores produced on wheat plants are asexual, meaning that they are genetically identical to the parent unless a mutation occurs. However, given the very large number of spores produced, there is a high chance of any given single mutation arising. For further complexity, stem rust also has a sexual reproduction cycle on the alternate host, barberry, allowing new combinations of effectors to be generated. To learn more about stem rust, see this video by the Borlaug Global Rust Initiative.

Program Impacts

Guarev K, Poland J, Wulff B, et al. (2021) Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat Biotechnol DOI: 10.1038/s41587-021-01058-4

Luo M, Freedman R, Reuber T L, Steffenson B, Ayliffe M, et al. A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat. Nat Biotechnol 39, 561–566 (2021). DOI: 10.1038/s41587-020-00770-x

Li F, Upadhyaya N, Sperschneider J, Matny O, Nguyen-Phuc H, Mago R, Raley C, Miller ME, Silverstein KAT, Henningsen E, Hirsch CD, Visser B, Pretorius ZA, Steffenson B, Schwessinger B, Dodds PN, Figueroa M (2019). Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridization. Nature Communications, in press.  BioRxiv: biorxiv.org/content/10.1101/692640v1  doi:10.1101/692640

Plant nonhost resistance: paradigms and new environments. Current Opinion in Plant Biology 50: 104-113. doi: 10.1016/j.pbi.2019.03.011

Luo M, Li H, Chakraborty S, Morbitzer R, Rinaldo A, Upadhyaya N, Bhatt D, Louis S, Richardson T, Lahaye T, Ayliffe M. (2019) Efficient TALEN mediated gene editing in wheat. Plant Biotechnology Journal. DOI: 10.1111/pbi.13169.

Hickey LT, N Hafeez A, Robinson H, Jackson SA, Leal-Bertioli SCM, Tester M, Gao C, Godwin ID, Hayes BJ, Wulff BBH (2019) Breeding crops to feed 10 billion. Nat Biotechnol 37: 744-754. DOI: 10.1038/s41587-019-0152-9

Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, et al. (2019) Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol 37: 139-143. DOI: 10.1038/s41587-018-0007-9

Ghosh S, Watson A, Gonzalez-Navarro OE, Ramirez-Gonzalez RH, Yanes L, Mendoza-Suárez M, Simmonds J, Wells R, Rayner T, Green P, et al. (2018) Speed breeding in growth chambers and glasshouses for crop breeding and model plant research. Nat Protoc 13: 2944-2963. DOI: 10.1038/s41596-018-0072-z

Hatta AMM, Johnson R, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Arora S, Steuernagel B, et al. (2018) The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. BioRxiv DOI: 10.1101/374637

Bettgenhaeuser J, Gardiner M, Spanner R, Green P, Hernández-Pinzón I, Hubbard A, Ayliffe M, Moscou MJ. (2018). The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates. PLoS Genetics 14(9): e1007637. DOI: 10.1371/journal.pgen.1007637

Gilbert B, Bettgenhaeuser J, Upadhyaya N, Soliveres M, Singh D, Park RF, Moscou MJ, Ayliffe M. (2018). Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited. PLoS Genetics 14(9): e1007636.

Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J, Rey M-D, Hatta MAM, Hinchliffe A, Steed A, Reynolds D, et al. (2018) Speed breeding is a powerful tool to accelerate crop research and breeding. Nature Plants 4: 23-29. DOI: 10.1038/s41477-017-0083-8

Wulff BBH, Dhugga KS (2018) Wheat-the cereal abandoned by GM. Science 361: 451-452. DOI: 10.1126/science.aat5119

Chen J, Upadhyaya NM, Ortiz D, Sperschneider J, Li F, Bouton C, Breen S, Dong C, Xu B, Zhang X, et al. (2017). Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat. Science 358(6370): 1607-1610. DOI: 10.1126/science.aao4810 

Steuernagel B, Witek K, Jones JDG, Wulff BBH. (2017). MutRenSeq: A Method for Rapid Cloning of Plant Disease Resistance Genes. Methods Mol Biol 1659: 215-229. doi: 10.1007/978-1-4939-7249-4_19

Yu G, Champouret N, Steuernagel B, Olivera PD, Simmons J, Williams C, Johnson R, Moscou MJ, Hernández-Pinzón I, Green P, Sela H, Millet E, Jones JD, Ward ER, Steffenson BJ, Wulff BB (2017). Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis. Theoretical and Applied Genetics doi: 10.1007/s00122-017-2882-8. [Epub ahead of print]

Bevan MW, Uauy C, Wulff BB, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543: 346-354. DOI: 10.1038/nature22011

Figueroa M, Upadhyaya NM, Sperschneider J, Park RF, Szabo LJ, Steffenson B, Ellis JG, Dodds PN (2016). Changing the game: using integrative genomics to probe virulence mechanisms of the stem rust pathogen Puccinia graminis f. sp. tritici. Frontiers in Plant Science 7:205. doi:10.3389/fpls.2016.00205

Luo M, Gilbert B, Ayliffe M (2016). Applications of CRISPR/Cas9 technology for targeted mutagenesis, gene replacement and stacking of genes in higher plants. Plant Cell Reports 35:1439. doi: 10.1007/s00299-016-1989-8.

Steuernagel B, Periyannan S, Hernández-Pinzón I, Witek K, Rouse M, Yu G, Hatta A, Ayliffe M, Bariana H, Jones J, Lagudah E, and Wulff B (2016). Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nature Biotechnology 34:652 doi:10.1038/nbt.3543.

Dawson A, Ferguson J, Gardiner M, Green P, Hubbard A, and Moscou MJ (2016). Isolation and fine mapping of Rps6: an intermediate host resistance gene in barley to wheat stripe rust. Theoretical and Applied Genetics 129:831 doi:10.1007/s00122-015-2659-x.

Knight E, Binnie A, Draeger T, Moscou M, Rey M, Sucher J, Mehra S, King I, and Moore G (2015). Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh of Aegilops sharonensisTheoretical and Applied Genetics 148:1049 doi:10.1007/s00122-015-2489-x.

Dawson AM, Bettgenhaeuser J, Gardiner M, Green P, Hernández-Pinzón I, Hubbard A and Moscou MJ (2015). The development of quick, robust, quantitative phenotypic assays for describing the host–nonhost landscape to stripe rust. Frontiers in Plant Science 6:876. doi: 10.3389/fpls.2015.00876.

Patron N, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farre-Martinez G, Rogers C, Smith A. Hibberd J, Webb A, Locke J, Schornack S, Ajioka J, Baulcombe D, Zipfel C, Kamoun S, Jones J, Kuhn H, Robatzek S, van Esse HP, Oldroyd G, Sanders D, Martin C, Field R, O’Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loque D, Granell A, Tissier A, Shih P, Brutnell T, Quick P, Rischer H, Fraser P, Aharoni A, Raines C, South P, Ané JM, Hamberger B, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray J, Ntoukakis V, Schafer P, Denby K, Edwards K, Osbourn A, and Haselof J (2015). Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts. New Phytologist 208: 13–19. doi:10.1111/nph.13532.

Sandve SR, Marcussen T, Mayer K, Jakobsen KS, Heier L, Steuernagel B, Wulff BBH, Olsen OA (2015). Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D-genome. New Phytologist 208: 9–10. doi: 10.1111/nph.13487.

Steuernagel B, Jupe F, Witek K, Jones JDG, Wulff BBH (2015). NLR-parser: rapid annotation of plant NLR complements. Bioinformatics 31:1665-7. doi:10.1093/bioinformatics/btv005.

Fitzgerald TL, Powell JJ, Schneebeli K, Hsia MM, Gardiner DM, Bragg JN, McIntyre CL, Manners JM, Ayliffe M, Watt M, Vogel JP, Henry RJ, Kazan K (2015) Brachypodium as an emerging model for cereal-pathogen interactions. Annals of Botany 115:717-731.

Upadhyaya NM, Garnica DP, Karaoglu H, Nemri A, Sperschneider J, Xu B, Mago R, Cuomo CA, Rathjen JP, Park RF, Ellis JG, Dodds PN (2015). Comparative genomics of Australian stem rust isolates reveals extensive polymorphism in candidate effector genes. Frontiers in Plant Science 5: 543.

Upadhyaya N, Ellis JG, Dodds PN (2014). A bacterial Type III Secretion based delivery system for functional assays of fungal effectors in cereals. In Methods in Molecular Biology, Plant Pathogen Interactions: Methods and Protocols (ed P Birch, JT Jones, JIB Bos) Springer-Verlag New York, LLC. pp 277-290.

Garnica D, Nemri A, Upadhyaya N, Rathjen JP, Dodds PN (2014). The ins and outs of rust haustoria. PLoS Pathogens 10: e1004329.

Wulff BHH. and Moscou MJ (2014). Strategies for transferring resistance into wheat: from wide crosses to GM cassettes. Frontiers in Plant Science 5:692. doi: 10.3389/fpls.2014.00692.

Bettgenhaeuser J, Gilbert M, Ayliffe M, and Moscou MJ (2014). Nonhost resistance to rust pathogens – a continuation of continua. Frontiers in Plant Science 5:664. doi: 10.3389/fpls.2014.00664.

Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, International Wheat Genome Sequencing Consortium, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KF, Olsen OA (2014). Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092. doi: 10.1126/science.1250092.

International Wheat Genome Sequencing Consortium (IWGSC) (2014). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788. doi: 10.1126/science.1251788.

Sperschneider J, Ying E, Dodds PN, Gardiner DM, Upadhyaya NM, Singh KB, Manners JM, Taylor JM (2014). Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors. Frontiers in Plant Science 5: 372.

Gardiner DM, Stiller J, Upadhyaya NM, Ellis JG, Dodds PN, Manners JM (2014). Xanthomonas pathogenic on wheat and barley, a comparative and functional pathogenomics resource. PLoS ONE 9: e84995.

Bouyioukos C, Moscou MJ, Champouret N, Hernández-Pinzón I, Ward ER, and Wulff BBH (2013). Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the Sitopsis section. PLoS ONE 8: e72782.

Ayliffe M, Singh D, Park R, Moscou M, and Pryor T (2013). The infection of Brachypodium distachyon with selected grass rust pathogens. Molecular Plant-Microbe Interactions 26: 946-957.

Duplessis S, Joly D, Dodds PN. (2012). Rust effectors. In “Effectors in Plant-Microbe Interactions” (eds F Martin and S Kamoun) Wiley-Blackwell Press, pages 155-194.

Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Wu Y, Lonardi S, Castillo AM, Chao S, Cistué L, Cuesta-Marcos A, Forrest K, Hayden MJ, Hayes PM, Horsley RD, Kleinhofs A, Moody D, Sato K, Vallés MP, Wulff BBH, Muehlbauer GJ, Doležel J, and Close TJ (2011). An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers. The Plant Genome 4: 238-249.

Champouret N, Moscou MJ, Bouyioukos C, Steuernagel B, Hernandez-Pinzon I, Green P, Kaufman J, Olivera PD, Pretorius Z, Millet E, Steffenson BJ, Ward ER & Wulff BBH (2011). A pipeline for cloning resistance genes effective against African stem rust races from the diploid wheat relative Aegilops sharonensis In: Proc Borlaug Global Rust Initiative June 13–19. McIntosh, R.

Ayliffe M, Rosangela D, Mago R, White R, Talbot M, Pryor T, (2011). Nonhost resistance of rice to rust pathogens. Molecular Plant-Microbe Interactions 24: 1143-1155.

Ayliffe M, Jin Y, Kang Z, Persson M, Steffenson B, Leung H, (2011). Determining the basis of nonhost resistance in rice to cereal rusts. Euphytica 179: 33-40.

Dodds PN, Lawrence GJ, Mago R, Ayliffe MA, Upadhyaya N, Szabo L, Park R and Ellis JG (2010). Advances in host-pathogen molecular interactions: rust effectors as targets for recognition. In R.A. McIntosh (ed.), Borlaug Global Rust Initiative 2009 Technical Workshop Proceedings. 17-20 March 2009. Cd. Obregón, Mexico: BGRI pages 49-54.

Ayliffe M, Jin Y, Steffenson B, Kang Z, Wang S, Leung H, In: McIntosh, R.A. (2010). Molecular-genetic dissection of rice nonhost resistance to wheat stem rust In R.A. McIntosh (ed.), Borlaug Global Rust Initiative 2009 Technical Workshop Proceedings. 17-20 March 2009. Cd. Obregón, Mexico: BGRI